The various Pre-Shinra towns on the central continent of Gaia fit into three broad categories. Firstly, there are the defensive emplacements, which describes Nibelheim, Cosmo Canyon and Corel. All of these sit either across or near key routes through their region, and it could be postulated that each of them is set up to act as a barrier against Jenovan invasion from the Northern continent. Secondly, there are the port towns - Junon and Costa del Sol. With only one port on each continent (and apparently none in Wutai) it provides a clear way of cutting off a further path of possible infection. Finally, there are the gene banks - Gongaga, Midgar, and Mideel. Each of these towns are located inland, in isolated areas (Gongaga and Mideel are surrounded by jungle, Midgar by mountains) and away from any obvious features which would indicate a clear passage to these towns. They're isolated by design, places where the last remnants of humanity could flee and hide, and build up numbers again.
Icicle Village is another of the defensive towns - it's set up across the one clear path from the crater to the main part of the northern continent, but it's also the best place to watch for any encroachment from the Calamity. This accounts for why Ifalna was originally living there.